clinicedc 2.0.38__py3-none-any.whl → 2.0.40__py3-none-any.whl

edc_data_manager/handlers/handlers.py

@@ -1,3 +1,8 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import TYPE_CHECKING
+
 import arrow
 from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
@@ -15,6 +20,12 @@ from edc_visit_tracking.utils import (
 from ..constants import AUTO_RESOLVED
 from ..models import DataQuery
 
+if TYPE_CHECKING:
+    from edc_registration.models import RegisteredSubject
+    from edc_visit_schedule.visit_schedule import VisitSchedule
+
+    from ..models import QueryRule
+
 
 class QueryRuleHandlerError(Exception):
     pass
@@ -57,11 +68,12 @@ class QueryRuleHandler:
 
     def __init__(
         self,
-        query_rule_obj=None,
-        registered_subject=None,
-        visit_schedule_obj=None,
-        visit_code_sequence=None,
-        now=None,
+        *,
+        query_rule_obj: QueryRule,
+        registered_subject: RegisteredSubject,
+        visit_schedule_obj: VisitSchedule,
+        now: datetime,
+        visit_code_sequence: int | None = None,
     ):
         self._field_values = {}
         self._model_obj = None

edc_data_manager/models/query_rule.py

@@ -7,7 +7,7 @@ from django.db import models
 from django.db.models.deletion import PROTECT
 from django.template.loader import render_to_string
 
-from edc_constants.constants import NORMAL
+from edc_constants.constants import NORMAL, NULL_STRING
 from edc_model.models import BaseUuidModel, HistoricalRecords
 from edc_visit_schedule.constants import DAYS, HOURS, MONTHS, WEEKS
 
@@ -31,7 +31,7 @@ class QueryRuleManager(models.Manager):
 def get_rule_handler_choices(model_name=None):
     choices = []
     for rule_handler in site_data_manager.get_rule_handlers(model_name=model_name):
-        choices.append((rule_handler.name, rule_handler.display_name))
+        choices.append((rule_handler.name, rule_handler.display_name))  # noqa: PERF401
     return tuple(choices) or (
         (DEFAULT_RULE_HANDLER, DEFAULT_RULE_HANDLER.replace("_", " ").title()),
     )
@@ -105,7 +105,7 @@ class QueryRule(BaseUuidModel):
 
     title = models.CharField(max_length=150, unique=True)
 
-    reference_model = models.CharField(max_length=150, null=True, editable=False)
+    reference_model = models.CharField(max_length=150, default=NULL_STRING, editable=False)
 
     sender = models.ForeignKey(
         DataManagerUser,
@@ -152,7 +152,7 @@ class QueryRule(BaseUuidModel):
 
     query_text = models.TextField(
         help_text="Generic query text for auto-generated queries.",
-        null=True,
+        default=NULL_STRING,
         blank=True,
     )
 
@@ -192,7 +192,7 @@ class QueryRule(BaseUuidModel):
 
     reference = models.CharField(max_length=36, default=uuid4, unique=True)
 
-    comment = models.TextField(null=True, blank=True)
+    comment = models.TextField(default=NULL_STRING, blank=True)
 
     objects = QueryRuleManager()
 
@@ -209,13 +209,13 @@ class QueryRule(BaseUuidModel):
     def natural_key(self):
         return (self.title,)
 
-    natural_key.dependencies = [
+    natural_key.dependencies = (
         "edc_data_manager.CrfDataDictionary",
         "edc_data_manager.DataManagerUser",
         "edc_data_manager.QueryUser",
         "edc_data_manager.queryvisitschedule",
         "edc_data_manager.RequisitionPanel",
-    ]
+    )
 
     @property
     def rendered_query_text(self) -> str:

edc_data_manager/navbar_item.py

@@ -5,5 +5,5 @@ dm_navbar_item = NavbarItem(
     title="Data Management",
     label="DM",
     codename="edc_data_manager.nav_data_manager_section",
-    url_name="edc_data_manager:home_url",
+    url_with_namespace="edc_data_manager:home_url",
 )

edc_data_manager/rule/query_rule_wrapper.py

@@ -87,7 +87,7 @@ class QueryRuleWrapper:
         return getattr(
             self.subject_identifiers,
             "all",
-            lambda: [{"subject_identifier": s for s in self.subject_identifiers}],
+            lambda: [{"subject_identifier": s} for s in self.subject_identifiers],
         )
 
     @staticmethod

edc_data_manager/rule/rule_runner.py

@@ -21,7 +21,7 @@ class RuleRunner:
     def __init__(
         self,
         query_rule_obj: QueryRule = None,
-        now: datetime = None,
+        now: datetime | None = None,
         verbose: bool | None = None,
     ):
         self.query_rule_obj = query_rule_obj  # query rule model instance
@@ -55,11 +55,11 @@ class RuleRunner:
 
     def run_one(
         self,
-        subject_identifier: str = None,
-        visit_schedule_name: str = None,
-        schedule_name: str = None,
-        visit_code: str = None,
-        timepoint: Decimal = None,
+        subject_identifier: str,
+        visit_schedule_name: str,
+        schedule_name: str,
+        visit_code: str,
+        timepoint: Decimal,
     ):
         visit_schedule_obj = QueryVisitSchedule.objects.get(
             visit_schedule_name=visit_schedule_name,

edc_device/navbars.py

@@ -8,7 +8,7 @@ device.register(
         label="device",
         fa_icon="fa-calculator",
         codename="edc_navbar.nav_edc_device",
-        url_name="edc_device:home_url",
+        url_with_namespace="edc_device:home_url",
     )
 )
 

edc_export/navbars.py

@@ -7,7 +7,7 @@ navbar.register(
         name="export",
         label="Export",
         fa_icon="fa-file-export",
-        url_name="edc_export:home_url",
+        url_with_namespace="edc_export:home_url",
         codename="edc_navbar.nav_export",
     )
 )
@@ -16,7 +16,7 @@ navbar.register(
     NavbarItem(
         name="data_request",
         label="Export Admin",
-        url_name="edc_export:admin:index",
+        url_with_namespace="edc_export:admin:index",
         codename="edc_navbar.nav_export",
     )
 )

edc_glucose/model_mixin_factories/fasting_model_mixin_factory.py

@@ -7,7 +7,7 @@ from edc_model.validators import hm_validator
 
 
 def fasting_model_mixin_factory(
-    prefix: str = None, verbose_names: dict | None = None, **kwargs
+    prefix: str | None = None, verbose_names: dict | None = None, **kwargs
 ):
     prefix = "" if prefix is None else f"{prefix}_"
     verbose_names = verbose_names or {}

edc_identifier/identifier.py

@@ -96,16 +96,13 @@ class Identifier:
     @property
     def last_identifier(self):
         """Returns the last identifier in the identifier model."""
-        try:
-            instance = (
-                self.identifier_model_cls.objects.filter(identifier_type=self.name)
-                .order_by("-sequence_number")
-                .first()
-            )
-        except AttributeError:
-            return None
-        else:
+        if instance := (
+            self.identifier_model_cls.objects.filter(identifier_type=self.name)
+            .order_by("-sequence_number")
+            .first()
+        ):
             return instance.identifier
+        return None
 
     def remove_separator(self, identifier):
         """Returns the identifier after removing the separator.

edc_lab_dashboard/dashboard_urls.py

@@ -1,14 +1,18 @@
 """To customize any of the values below,
 use settings.LAB_DASHBOARD_URL_NAMES.
+
+These have nothing to do with url_names dictionary
 """
 
+import contextlib
+
 from django.conf import settings
 
 dashboard_urls = dict(
     aliquot_listboard_url="edc_lab_dashboard:aliquot_listboard_url",
-    dashboard_url="edc_lab_dashboard:home_url",
+    lab_dashboard_home_url="edc_lab_dashboard:home_url",
     # home_url="edc_lab_dashboard:home_url",
-    listboard_url="edc_lab_dashboard:requisition_listboard_url",
+    # listboard_url="edc_lab_dashboard:requisition_listboard_url",
     manage_box_listboard_url="edc_lab_dashboard:manage_box_listboard_url",
     manage_manifest_listboard_url="edc_lab_dashboard:manage_manifest_listboard_url",
     manifest_listboard_url="edc_lab_dashboard:manifest_listboard_url",
@@ -32,7 +36,5 @@ dashboard_urls = dict(
     verify_box_item_form_action_url="edc_lab_dashboard:verify_box_item_form_action_url",
 )
 
-try:
+with contextlib.suppress(AttributeError):
     dashboard_urls.update(**settings.LAB_DASHBOARD_URL_NAMES)
-except AttributeError:
-    pass

edc_lab_dashboard/middleware.py

@@ -1,38 +1,31 @@
 from django.conf import settings
-
+from edc_dashboard.middleware_mixins import EdcTemplateMiddlewareMixin
 from edc_lab.constants import SHIPPED
 
 from .dashboard_templates import dashboard_templates
 from .dashboard_urls import dashboard_urls
 
 
-class DashboardMiddleware:
+class DashboardMiddleware(EdcTemplateMiddlewareMixin):
     def __init__(self, get_response):
         self.get_response = get_response
 
     def __call__(self, request):
-        response = self.get_response(request)
-        return response
+        self.check_for_required_request_attrs(request)
+        return self.get_response(request)
 
     def process_view(self, request, *args):
+        lab_dashboard_urls = getattr(settings, "LAB_DASHBOARD_URL_NAMES", {})
+        dashboard_urls.update(**lab_dashboard_urls)
         request.url_name_data.update(**dashboard_urls)
-        try:
-            url_name_data = settings.LAB_DASHBOARD_URL_NAMES
-        except AttributeError:
-            pass
-        else:
-            request.url_name_data.update(**url_name_data)
 
-        template_data = dashboard_templates
-        try:
-            template_data.update(settings.LAB_DASHBOARD_BASE_TEMPLATES)
-        except AttributeError:
-            pass
+        template_data = getattr(settings, "LAB_DASHBOARD_BASE_TEMPLATES", {})
+        template_data.update(**dashboard_templates)
         request.template_data.update(**template_data)
 
     def process_template_response(self, request, response):
-        if response.context_data:
+        if getattr(response, "context_data", None):
+            response.context_data.update(SHIPPED=SHIPPED)
             response.context_data.update(**request.url_name_data)
             response.context_data.update(**request.template_data)
-            response.context_data.update(SHIPPED=SHIPPED)
         return response

edc_lab_dashboard/navbars.py

@@ -8,7 +8,7 @@ specimens_navbar = NavbarItem(
     title="Specimens",
     fa_icon="fa-flask",
     codename="edc_lab_dashboard.nav_lab_section",
-    url_name="requisition_listboard_url",
+    url_names_key="requisition_listboard_url",
 )
 
 _specimens_navbar = copy(specimens_navbar)
@@ -22,7 +22,7 @@ navbar.register(
         name="requisition",
         label="Requisition",
         codename="edc_lab_dashboard.nav_lab_requisition",
-        url_name="requisition_listboard_url",
+        url_names_key="requisition_listboard_url",
     )
 )
 
@@ -31,7 +31,7 @@ navbar.register(
         name="receive",
         label="Receive",
         codename="edc_lab_dashboard.nav_lab_receive",
-        url_name="receive_listboard_url",
+        url_names_key="receive_listboard_url",
     )
 )
 
@@ -40,7 +40,7 @@ navbar.register(
         name="process",
         label="Process",
         codename="edc_lab_dashboard.nav_lab_process",
-        url_name="process_listboard_url",
+        url_names_key="process_listboard_url",
     )
 )
 
@@ -49,7 +49,7 @@ navbar.register(
         name="pack",
         label="Pack",
         codename="edc_lab_dashboard.nav_lab_pack",
-        url_name="pack_listboard_url",
+        url_names_key="pack_listboard_url",
     )
 )
 
@@ -58,7 +58,7 @@ navbar.register(
         name="manifest",
         label="Manifest",
         codename="edc_lab_dashboard.nav_lab_manifest",
-        url_name="manifest_listboard_url",
+        url_names_key="manifest_listboard_url",
     )
 )
 
@@ -67,7 +67,7 @@ navbar.register(
         name="aliquot",
         label="Aliquot",
         codename="edc_lab_dashboard.nav_lab_aliquot",
-        url_name="aliquot_listboard_url",
+        url_names_key="aliquot_listboard_url",
     )
 )
 
@@ -76,7 +76,7 @@ navbar.register(
         name="result",
         label="Result",
         codename="edc_lab_dashboard.nav_lab_result",
-        url_name="result_listboard_url",
+        url_names_key="result_listboard_url",
     )
 )
 
@@ -86,7 +86,7 @@ navbar.register(
         title="Specimens",
         fa_icon="fa-flask",
         codename="edc_lab_dashboard.nav_lab_section",
-        url_name="requisition_listboard_url",
+        url_names_key="requisition_listboard_url",
         active=True,
     )
 )

edc_lab_dashboard/templates/edc_lab_dashboard/listboard/tags/status_column.html

@@ -0,0 +1,7 @@
+{% for label, status in options.items %}
+  {% if status %}
+      <span class="text text-success"><i class="fas fa-check-circle fa-lg" title="{{ label|title }}"></i></span>
+  {% else %}
+      <span class="text text-danger"><i class="fas fa-times-circle fa-lg" title="Not {{ label }}"></i></span>
+  {% endif %}
+{% endfor %}

edc_lab_dashboard/urls.py

@@ -1,5 +1,4 @@
 from django.urls.conf import path, re_path
-
 from edc_dashboard.url_names import url_names
 
 from .dashboard_urls import dashboard_urls
@@ -97,7 +96,7 @@ urlpatterns = [
         name="verify_box_listboard_url",
     ),
     re_path(
-        "listboard/box/(?P<action_name>verify)/" "(?P<position>[0-9]+)/$",
+        "listboard/box/(?P<action_name>verify)/(?P<position>[0-9]+)/$",
         VerifyBoxListboardView.as_view(),
         name="verify_box_listboard_url",
     ),
@@ -158,9 +157,7 @@ urlpatterns = [
         name="manage_box_item_form_action_url",
     ),
     re_path(
-        "box/(?P<box_identifier>[A-Z0-9]+)/"
-        "(?P<action_name>verify)/"
-        "(?P<position>[0-9]+)/$",
+        "box/(?P<box_identifier>[A-Z0-9]+)/(?P<action_name>verify)/(?P<position>[0-9]+)/$",
         VerifyBoxItemView.as_view(),
         name="verify_box_item_form_action_url",
     ),

edc_lab_dashboard/view_mixins/form_action_view_mixin.py

@@ -2,7 +2,6 @@ from typing import Any
 
 from django.urls.base import reverse
 from django.views.generic.base import ContextMixin
-
 from edc_dashboard.url_names import url_names
 
 
@@ -14,7 +13,7 @@ class FormActionViewMixin(ContextMixin):
     action_name = None
     form_action_name = "form_action"
     form_action_selected_items_name = "selected_items"
-    form_action_url = None
+    form_action_url = None  # url name
 
     def get_context_data(self, **kwargs) -> dict[str, Any]:
         kwargs.update(

edc_lab_dashboard/views/action_views/action_view.py

@@ -23,13 +23,13 @@ class ActionView(TemplateView):
     aliquot, etc.
     """
 
-    form_action_selected_items_name = "selected_items"
-    post_action_url = None  # key exists in url_names
-    redirect_querystring = {}
-    template_name = dashboard_templates.get("home_template")
-    valid_form_actions = []
+    form_action_selected_items_name: str = "selected_items"
+    post_action_url: str = None  # key exists in url_names
+    redirect_querystring: dict = {}  # noqa: RUF012
+    template_name: str = dashboard_templates.get("home_template")
+    valid_form_actions: tuple[str, ...] = ()
 
-    navbar_name = "specimens"
+    navbar_name: str = "specimens"
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)

edc_lab_dashboard/views/action_views/aliquot_view.py

@@ -9,7 +9,7 @@ from .action_view import ActionView
 
 class AliquotView(EdcViewMixin, LabPrintersMixin, ActionView):
     post_action_url = "aliquot_listboard_url"
-    valid_form_actions = ["print_labels"]
+    valid_form_actions = ("print_labels",)
     action_name = "aliquot"
     label_cls = AliquotLabel
 

edc_lab_dashboard/views/action_views/manage_box_item_view.py

@@ -2,7 +2,6 @@ from django.contrib import messages
 from django.core.exceptions import ObjectDoesNotExist
 from django.urls import reverse
 from django.utils.html import format_html
-
 from edc_dashboard.url_names import url_names
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_lab import SHIPPED
@@ -13,8 +12,8 @@ from .action_view import ActionView
 
 
 class ManageBoxItemView(EdcViewMixin, BoxViewMixin, ActionView):
-    post_action_url = "manage_box_listboard_url"
-    valid_form_actions = ["add_item", "renumber_items", "remove_selected_items"]
+    post_action_url = "manage_box_listboard_url"  # url_name
+    valid_form_actions = ("add_item", "renumber_items", "remove_selected_items")
 
     @property
     def url_kwargs(self):

edc_lab_dashboard/views/action_views/manage_manifest_view.py

@@ -16,7 +16,7 @@ class ManageManifestViewError(Exception):
 
 class ManageManifestView(EdcViewMixin, ManifestViewMixin, ActionView):
     post_action_url = "manage_manifest_listboard_url"
-    valid_form_actions = ["add_item", "remove_selected_items"]
+    valid_form_actions = ("add_item", "remove_selected_items")
 
     @property
     def url_kwargs(self):

edc_lab_dashboard/views/action_views/manifest_view.py

@@ -13,11 +13,11 @@ from .action_view import ActionView
 
 class ManifestView(EdcViewMixin, ManifestViewMixin, LabPrintersMixin, ActionView):
     post_action_url = "manifest_listboard_url"
-    valid_form_actions = [
+    valid_form_actions = (
         "remove_selected_items",
         "print_labels",
         "ship_selected_items",
-    ]
+    )
     label_cls = ManifestLabel
 
     def process_form_action(self, request=None):

edc_lab_dashboard/views/action_views/pack_view.py

@@ -14,11 +14,11 @@ from .action_view import ActionView
 
 class PackView(EdcViewMixin, LabPrintersMixin, ActionView):
     post_action_url = "pack_listboard_url"
-    valid_form_actions = [
+    valid_form_actions = (
         "add_selected_to_manifest",
         "remove_selected_items",
         "print_labels",
-    ]
+    )
     label_cls = BoxLabel
 
     def __init__(self, **kwargs):

edc_lab_dashboard/views/action_views/process_view.py

@@ -9,7 +9,7 @@ from .action_view import ActionView
 
 class ProcessView(EdcViewMixin, ProcessRequisitionViewMixin, ActionView):
     post_action_url = "process_listboard_url"
-    valid_form_actions = ["process"]
+    valid_form_actions = ("process",)
     action_name = "process"
     label_cls = AliquotLabel
 

edc_lab_dashboard/views/action_views/receive_view.py

@@ -14,7 +14,7 @@ from .action_view import ActionView
 
 class ReceiveView(EdcViewMixin, ProcessRequisitionViewMixin, ActionView):
     post_action_url = "receive_listboard_url"
-    valid_form_actions = ["receive", "receive_and_process"]
+    valid_form_actions = ("receive", "receive_and_process")
     label_cls = AliquotLabel
     specimen_cls = Specimen
 

edc_lab_dashboard/views/action_views/requisition_view.py

@@ -11,7 +11,7 @@ from .action_view import ActionView
 
 class RequisitionView(EdcViewMixin, ProcessRequisitionViewMixin, ActionView):
     post_action_url = "requisition_listboard_url"
-    valid_form_actions = ["print_labels", "print_aliquot_labels"]
+    valid_form_actions = ("print_labels", "print_aliquot_labels")
     action_name = "requisition"
     label_cls = RequisitionLabel
 

edc_lab_dashboard/views/action_views/verify_box_item_view.py

@@ -11,7 +11,7 @@ from .action_view import ActionView
 class VerifyBoxItemView(EdcViewMixin, BoxViewMixin, ActionView):
     post_action_url = "verify_box_listboard_url"
     box_item_failed = False
-    valid_form_actions = ["verify_item", "reset_box", "verify_box"]
+    valid_form_actions = ("verify_item", "reset_box", "verify_box")
 
     @property
     def url_kwargs(self):

edc_lab_dashboard/views/listboard_views/manage_box_listboard_view.py

@@ -2,7 +2,6 @@ from copy import copy
 from typing import Any
 
 from django.urls.base import reverse
-
 from edc_dashboard.url_names import url_names
 
 from .base_box_item_listboard_view import BaseBoxItemListboardView
@@ -10,13 +9,13 @@ from .base_box_item_listboard_view import BaseBoxItemListboardView
 
 class ManageBoxListboardView(BaseBoxItemListboardView):
     action_name = "manage"
-    form_action_url = "manage_box_item_form_action_url"
-    listboard_url = "manage_box_listboard_url"
+    form_action_url = "manage_box_item_form_action_url"  # url_name
+    listboard_url = "manage_box_listboard_url"  # url_name
     listboard_template = "manage_box_listboard_template"
-    verify_box_listboard_url = "verify_box_listboard_url"
+    verify_box_listboard_url = "verify_box_listboard_url"  # url_name
     listboard_model = "edc_lab.boxitem"
     navbar_selected_item = "pack"
-    search_form_url = "manage_box_listboard_url"
+    search_form_url = "manage_box_listboard_url"  # url_name
 
     @property
     def url_kwargs(self):

edc_lab_dashboard/views/listboard_views/manifest_listboard_view.py

@@ -11,15 +11,15 @@ from .base_listboard_view import BaseListboardView
 class ManifestListboardView(BaseListboardView):
     navbar_selected_item = "manifest"
 
-    form_action_url = "manifest_form_action_url"
-    listboard_url = "manifest_listboard_url"
+    form_action_url = "manifest_form_action_url"  # url_name
+    listboard_url = "manifest_listboard_url"  # url_name
     listboard_template = "manifest_listboard_template"
     listboard_model = "edc_lab.manifest"
     listboard_view_permission_codename = "edc_lab_dashboard.view_lab_manifest_listboard"
     listboard_view_only_my_permission_codename = None
     listboard_view_filters = ManifestListboardViewFilters()
-    search_form_url = "manifest_listboard_url"
-    print_manifest_url = "print_manifest_url"
+    search_form_url = "manifest_listboard_url"  # url_name
+    print_manifest_url = "print_manifest_url"  # url_name
 
     def get_context_data(self, **kwargs) -> dict[str, Any]:
         kwargs.update(
@@ -31,8 +31,7 @@ class ManifestListboardView(BaseListboardView):
 
     def get(self, request, *args, **kwargs):
         if request.GET.get("pdf"):
-            response = self.print_manifest()
-            return response
+            return self.print_manifest()
         return super().get(request, *args, **kwargs)
 
     @property

edc_lab_dashboard/views/listboard_views/process_listboard_view.py

@@ -6,7 +6,6 @@ from django.apps import apps as django_apps
 from django.urls import reverse
 from django.utils.html import format_html
 from django.utils.safestring import mark_safe
-
 from edc_constants.constants import YES
 from edc_dashboard.url_names import url_names
 
@@ -20,13 +19,13 @@ app_config = django_apps.get_app_config("edc_lab_dashboard")
 
 class ProcessListboardView(RequisitionListboardView):
     action_name = "process"
-    form_action_url = "process_form_action_url"
+    form_action_url = "process_form_action_url"  # url_name
     listboard_template = "process_listboard_template"
-    listboard_url = "process_listboard_url"
+    listboard_url = "process_listboard_url"  # url_name
     listboard_view_permission_codename = "edc_lab_dashboard.view_lab_process_listboard"
     listboard_view_only_my_permission_codename = None
     navbar_selected_item = "process"
-    search_form_url = "process_listboard_url"
+    search_form_url = "process_listboard_url"  # url_name
 
     def get_queryset_filter_options(self, request, *args, **kwargs) -> tuple[Q, dict]:
         q_object, options = super().get_queryset_filter_options(request, *args, **kwargs)
@@ -34,7 +33,7 @@ class ProcessListboardView(RequisitionListboardView):
         return q_object, options
 
     def get_empty_queryset_message(self):
-        href = reverse(url_names.get("pack_listboard_url"))
+        href = reverse(url_names.get(self.listboard_url))
         return format_html(
             "All specimens have been processed. Continue to "
             '<a href="{}" class="alert-link">packing</a>',